Integrated analysis of transcriptome, sRNAome and degradome sequencing provides insights into bacterial wilt resistance in potato.

BACKGROUND: Potato (Solanum tuberosum) is one of the most important global food crops. However, potato bacterial wilt, a destructive soil-borne disease caused by Ralstonia solanacearum, poses a huge threat to global potato production and quality, leading to serious economic losses worldwide. The wild potato species Solanum commersonii exhibits resistance to bacterial wilt, but the underlying molecular mechanisms remain largely obscure. RESULTS: In this study, we identified differentially expressed miRNAs (microRNAs), phased secondary short-interfering RNAs (phasiRNAs), along with their target transcripts, and elucidated the potential pathways involved in bacterial wilt resistance through high-throughput sequencing analyses of transcriptome, sRNAome, and degradome on normal and R. solanacearum-infected potato roots, which were collected from the susceptible diploid potato clone S. tuberosum group Phureja SP15-65 and the resistant diploid S. commersonii germplasm CM804. The results revealed that 3,434 and 1,045 differentially expressed genes (DEGs) were identified in susceptible SP15-65 and resistant CM804, respectively, with 7,652 DEGs identified between SP15-65 and CM804 upon pathogen inoculation. 23 transcripts specifically expressed in CM804 were identified to be responsive to R. solanacearum infection. Functional enrichment analysis of DEGs revealed that mitogen-activated protein kinase (MAPK) activation, reactive oxygen species (ROS) generation, calcium signaling, hormone signaling, secondary metabolism, and transcriptional reprogramming for defense were potential pathways in potato root response to R. solanacearum infection. Furthermore, 115 unique known and 147 putative novel miRNAs showed differential expression in SP15-65 or CM804 after pathogen infection. Among these differentially expressed miRNAs, some miR482, miR6024, and miR390 family members triggered the biosynthesis of phasiRNAs through the cleavage of phasiRNA-generating (PHAS) precursor transcripts, as validated by degradome-seq. The resulting phasiRNAs directed the cleavage of their downstream target mRNAs. Six miRNA-mRNA pairs and four pairs of phasiRNA-mRNA displayed negatively correlated expression changes, which may be related to bacterial wilt resistance in potato. CONCLUSIONS: This study sheds lights on the regulatory roles of small RNAs in potato resistance against bacterial wilt, and will provide a theoretical foundation for the cultivation of disease-resistant potato varieties.